The Clean Up Begins
by Blackcat509
Summary: Being the leader of Atlantis means your duties are never done, even when you are on the edge of collapsing from exhaustion. Tag to The Siege 1, 2, & 3. I guess you could call it Sparky if you stand on your head and read it in a mirror it's that mild.


**The Siege of City was over, now, the clean up begins.**

**Spoilers – The Siege 1, 2 & 3**

The Siege of the City was over, now, the clean up begins. The fear and adrenaline had drained away with departure of the Hive ships, to be replaced with euphoria and relief that they would live to see another day. Soldiers and civilians alike stood in wonder, gazing out at the ocean that should have witnessed their destruction.

Every section of the City seemed to have taken a hit, be it internally or externally or both. Somewhere on the East pier smoke still bloomed where a Dart had impacted, easily hidden under the shield turned cloak. Water spilled from the Ancient wall designs that had taken impacts from bullets when the Wraith had attempted to take the City from the inside.

As soon as the cloak had gone up and it was determined that the Wraith had gone on their merry way, Elizabeth went straight for the City wide comms to address her people. As the speakers came to life everyone froze, listening to the relived tone of their leaders voice.

"This is Weir. We have successfully cloaked the City and the Wraith have left. Well done everyone." With that she paused to allow the resounding cheers and applause to die down. "That isn't to say our job is done, our City is in a mess and more importantly our people need taking care of. I'm sure you can all find away to make yourselves useful. The Daedalus will be returning soon to help with the clean-up operation so that should allow many of you to get some well deserved rest but until then I hope you all will continue to act with the determination and strength you have shown over the past few days." As soon as the comms were shut down activity returned.

Immediately those around Elizabeth turned towards her, looking for her input on what should be tackled first.

"Rodney I want you to work on getting as many of the off-line systems up and running again, get whoever you need to help. Chuck, can you start organising repair teams to survey the structural damage and prioritize repairs to the City. Major, gather some security teams and run another sweep of the base. I want to make sure that any injured make it to the infirmary and that there are no Wraith left running around with the internal sensors being off-line. Also any Wraith bodies that you do find need moving to the morgue. Lets get it done."

Turning away, Elizabeth made for the stairs only to hear a set of heavy boots following her.

"Elizabeth." John's voice was demanding, and she knew what he wanted. " I want to get an off-world team ready so we can go and track down Ford, someone else can lead the security teams. Lorne could -"

"No, John right now I need you here."

"Elizabeth, he's a member of my team and I don't leave anyone behind." At his tone Elizabeth spun round to face him, her green eyes shining with pain and grief.

"I understand that Major, but right now the members of this expedition need you here to help put the City back together and to have someone to turn to when they don't know what to do next." She paused to gauge his reaction and catch her breath. "I want to send a team out there as much as you do but right now it just isn't possible. I'm sorry John, but the expedition comes first." She only just caught his nod of agreement, but easily heard him ordering security personnel to the gate room as she returned to her original path down the stairs and out of the control room.

The corridors of Atlantis were in chaos, people working together to move equipment out of the way and taking stock of damage. Already the thousands of bullet casing were being cleaned up, but still Elizabeth had to be careful of where she placed her feet to so she didn't slip on casings that had been ejected into the halls. In some areas the windows had exploded inwards leaving the area cold and breezy as night set in. Despite the state of the City people were in high spirits as she passed them always offering a warm smile.

If she'd thought that the rest of Atlantis was buzzing with activity it all seemed to be in slow motion compared to the infirmary. It took a moment before she could even see Dr. Beckett among the mass of people. Slowly she made her way over to him stopping and checking on many of the injured personnel in her way in an attempt to offer comfort. For a moment she stopped and talked to a group of injured Athosians and thank them in their efforts in protecting the city when Dr. Beckett noticed her and immediately walked over.

"Elizabeth, are ya all right? Your not hurt are ya?" His Scottish accent carried concern.

"No Carson, I'm fine. I just wanted to come down and see how your doing."

"Aye we're a little run off our feet but there seems to be less injured coming in now, seems like most have made it here already, but we ran out of beds hours ago, we've just ended up putting the less urgent cases in chairs or rolling out mattresses on the floor." He said indicating the patients that were between beds or leaning against walls. "It would have been better if the Daedalus could have taken some of the patients but when they went after those Hive ships they decided it would better if they left them here."

"All right, I'll find you some more people to come and help out down here and as soon as the Daedalus arrives I'll have some of the wounded moved there to take some of the pressure of you down here. Is there anything I can do to help?"

"Aye that'd be grand but right now there isn't much you can do but talk to people, keep them going until I can find someone to treat them." The shout of one of his nurses had him moving away with and apologetic smile.

Elizabeth's ear piece buzzed to life, making her jump at the panic tones of Rodney McKay. "Elizabeth, you need to come to the control room now. We have a problem."

"I'm on my way." Slowly she turned and dragged her tired body back in the direction of the control room.

As she entered, McKay almost ran down the stairs in his panic, the first words out of his mouth being, "they're not all dead!"

"Rodney, I don't understand, what aren't all dead?"

"The Wraith."

"What do you mean." She shouted at him, "Zelenka said the last one died trying to detonate a bomb somewhere in the City. How can there be more?" He seemed a little taken a back by her outburst but explained anyway.

"When that Wraith blew himself to bits a group of others must have knocked the internal sensors of so they wouldn't be detected. It was a ploy. That damned Wraith blew himself up so the others wouldn't be detected. I mean why, why the hell would he-

"Rodney."It was best to cut him off early before he got to deep into a rant, besides there were more important issues at the moment. "Contact Major Sheppard and help him coordinate his teams to find these Wraith before they can do anymore damage. Or worse."

"What could be worse than having Wraith running around the city." His tone was smug but confused.

"Oh I don't know," she snapped, "maybe that they try and contact the Hive ships we've just gotten rid of." At least the smirk was gone but that was sharp even by her standards. Immediately she turned to face him knowing she'd been too hard on him. "I'm sorry Rodney, that was uncalled for." He easily shrugged it of and began typing on his tablet. Knowing there was little more she could do Elizabeth turned in the direction of her office.

"Elizabeth, where are you going. You can't go out into the City until Sheppard finds those Wraith."

"I'm not Rodney, I'm going to my office. We lost a lot of people during the attack and they deserve a memorial before we send them home." She said with a sad smile on her face thinking of the people under her care who had died; feeling the weight of leadership falling heavily on her already worn shoulders.

"That'd be nice." Rodney nodded in agreement, as did many others in the control room.

She'd only been sat in her office for a few hours when Major Sheppard bounded up the stairs looking remarkably pleased with himself. Seeing Elizabeth in her office he headed straight over, not even bothering with knocking.

"We got 'em. No more Wraith in the City." At the news, Elizabeth leaned back in her chair and smiled up at him.

"Nice work Major."

"That's not all. I had some teams move all the dead Wraith into one of the rooms on level 38 so they're out of the way and any injured we found we had moved to the infirmary. Luckily there weren't that many."

"OK Major. When the Daedalus arrives go get some sleep. That's an order."

"Yes ma'am." He gave her one last smile and left her office. From where she was sat she could see Chuck was beckoning her over. Dragging her aching body out of her chair she headed over.

"Dr. Weir, we've completed structural surveys of the control tower and repairs shouldn't take too long. I've got teams working on it already and others on the south and east pier still surveying the damage but it looks like the Daedalus should be able to dock at the south pier when they arrive."

"Good, keep me informed. The Daedalus should be here any minute so when we get some relief crews, yourself, Rodney and Zelenka are off duty." All three nodded in turn.

She had just sat back down in her office where she was slowly compiling names of those who had lost their lives in the siege when her radio sparked to life.

"Elizabeth, it's Carson. Would you mind coming down to the infirmary?"

"I'm on my. What's wrong?"

"It's Colonel Everett, he's taken a turn for the worse and he's asking too speak to you." He paused for a moment and when he spoke again it was in a hushed tone. "I don't think he's got long left." Her pace increased to a near run at his last sentence. Beckett was waiting for her when she arrived and simply pointed her in the direction of the Colonel's bed. She headed over without comment.

"Colonel, how are you doing?" her question was filled with genuine concern, just as it had been for the rest of the expedition.

"It doesn't look like I'm going to be able to buy you that drink." Elizabeth had no words of comfort for Colonel Everett, there was nothing that could be done to save him from his fate. He seemed to sense this and continued speaking. "I want to apologise, Dr. Weir."

"Colonel, you have nothing to apologise for, I feel that it's me that should be apologising to you. You came here prepared to defend Atlantis from an enemy that wasn't your own and-"

"No." He cut her of sharply. "I came here fully aware of the risks and willing accepted them. What I want to apologise for is how I treated you when I first arrived on Atlantis. I didn't understand how military officers could put their faith in you and trust you to lead them when you have no military training. I underestimated the respect that everyone here gave you. I was wrong. I'm sorry for stepping on your toes and undermining your command." All she could do was nod in response. He looked up at her, seeming to take most of the energy from his frail form and smiled at her. "I know we didn't exactly see eye to eye when I first arrived here, but I've come to realise that your more important to this expedition than any military leader would be. However now, I can easily understand why you have the respect of everyone on this base."

"I wish you could have seen all the wonders you fought so hard to protect Colonel. I-" Once again her earpiece buzzed and Chuck's voice filled her head.

Laying his head back the pillow behind him he smiled once again. "Go, you people need you." She nodded and gave his hand a gentle squeeze and then left.

"Ma'am, the Daedalus has arrived. She's about to land on the south pier."

"Tell Colonel Caldwell I'll meet him there."

Twenty minutes later Elizabeth stepped out onto what was left of the south pier. Anything that had been built above ten metres had been damaged or had collapsed but the repair teams had already cleared a path and sealed of any exposed sections of the City with plastic sheeting. Several teams of people were already heading past her into the City to provide support wherever it was needed.

"Dr. Weir."

"Colonel Caldwell, thank you for your support. Right now we need it, unfortunately Atlantis is in a bit of a mess."

"I can see that. I've crews relieving most of your staff in the control room and the infirmary as well as security teams doing continuous sweeps of the base and medical teams moving some of the wounded to the Daedalus to take the pressure off you people."

"Thank you Colonel. Your help is most appreciated."

* * *

**12 hours later – 4 days since the siege began**

The Gate room was filled to capacity. Everyone sat in silence as Elizabeth stood at the small podium in front of the gate.

"We are her today to say goodbye to the those who gave their lives in defence of this City. These people died with honour and bravery and in defence of an idea, the idea that this City can one day be used for the betterment of mankind. The fact that we are still here and willing to carry on proves that they didn't die in vain. It's now up to us to make sure their spirit lives on in the work we do and that their sacrifices are never forgotten, and neither are their names." Slowly Elizabeth unfolded a piece of paper."

"Today we are here to remember Dr. Peter Grodin, Colonel Dillon Everett, Lt. Tanya West, Dr Hikari Chi..." The list was a long one, but not single name was left unsaid and not a single person moved during it.

"I would like to finish this with a minutes silence." At once everyone bowed their heads and when it was over people filed out, still in silence.

As the room emptied Elizabeth slumped against the podium. Every movement seemed to burn her already aching muscles.

"'Lizabeth, are you all right?"

"Yeah John, I'm fine." She said as she pulled herself upright and stepped down, back onto ground level. Both set of in the direction of the mess hall where a form of wake was being held in memory of the 48 Atlantis and SGC personnel and 17 Athosians who had lost their lives.

"That was beautiful you know, what you said back there."

"Thank you John, but somehow it just doesn't seem enough. 45 people died and what I say just doesn't seem good enough."

They continued to walk in silence until Elizabeth suddenly wavered on her feet. Instantly John grasped her shoulders to steady her and keep her upright.

"Whoa, 'Lizabeth?"

"I'm 'right."

"No your not, I'm taking you to the infirmary so Carson can have a look at you."

"John I'm fine, just a little tired. Let's just go to this wake." Gently she shrugged his hands of her shoulders and began walking again, only for he legs to almost give out from under her. Once again he caught her and kept her standing on her feet.

"When was the last time you slept Elizabeth?" He questioned.

"Erm, it was a few hours before the siege began. I think." Her speech was beginning to slur concerning John even further.

"That was almost five days ago!" He yelled at her. "That's it, I'm taking you to your quarters and contacting Dr. Beckett." She tried to protest but her body would comply and she was easlily being led towards her room. They were about half way there when he body finally gave up its battle against sleep and she dropped in John's arms.

John practically sprinted to Elizabeth's quarters, getting increasingly worried after she had collapsed and failed to respond to him on the journey there. Grateful for his link to the city, John had the door open before he even reached her room. Gently he lay her down on the bed and instantly contacted Carson on his radio. At hearing that Elizabeth had passed out, the Scottish doctor made it to her quarters in record time.

"What happened?" He asked.

"We were walking and then she began swaying on her feet and then half way here she collapsed. She hasn't respond to anything I've said."

"Why were ya both on your way to her quarters?"

"It's not what you think Doc. She said she hasn't slept since before the Wraith attack." Carson stopped his exam and turned to face him.

"She's going to be fine. I imagine she's suffering form exhaustion. In fact I guarantee it. Knowing Elizabeth she won't have stopped for food or sleep since this whole thing began and now that its over and the City is back in order her body has finally given in." Carson turned and headed for the door. "Let her rest Major, she needs it." Sheppard looked over at the Doctor and then back to the woman sleeping on the bed in front of him.

"I'm going to stay for a while, make sure she does get some rest." With an understanding smile Carson left and the door closed.

The Siege of the City was, so was the clean up. Now life returned to normal.

**A/N – This wasn't meant to be so long was just aiming for a nice short fic to ease me back into fanfiction as I haven't written in months and this is my first Atlantis fic. Please leave feedback and advice in comment... it's all greatly appreciated. :D**


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